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Generally, the port of Heraklion is connected daily with Piraeus with two ferry routes, run by modern, luxury and fast passenger-car ferries (E/C-O/C). It is also connected with the Dodecanese, while in the summer season there are daily itineraries to many islands of the Cyclades, with cruisers and/or ferries (E/C-t/h, O/C-t/h) boats.

All ships depart from the western part of the port and the I & II piers. Passengers can issue their tickets from the ticket counters of all ferry companies operating within the Passenger Terminal of the port, or next to the departure areas (for T/h only).